BACKGROUND: The physical activity levels of adult patients with cystic fibrosis hospitalised for an acute respiratory exacerbation is unknown. METHODS: A prospective observational study was undertaken. Physical activity levels were measured for a 24-h period using an activity monitor (SenseWear(®) Pro 3) during hospitalisation for an acute respiratory exacerbation and one month post-discharge. Measures of exercise tolerance and muscle strength were also recorded. RESULTS: Twenty-four patients completed the study. Most outcomes significantly increased from hospitalisation to one month post-discharge. Time spent doing physical activity (≥3 METs) increased from a mean ± SD of 95 ± 58 to 209 ± 111 min. CONCLUSIONS: Hospitalisation for an acute respiratory exacerbation was associated with less time spent performing physical activity compared to one month post-discharge. Physical activity levels were higher than anticipated, even during hospitalisation, suggesting an increased metabolic rate may have contributed to the physical activity levels documented. Activity level definitions for moderate intensity exercise that are based on higher MET levels seemed more appropriate in this patient setting. CLINICAL TRIAL REGISTRY: Australian New Zealand Clinical Trials Registry Number: ACTRN12610000595011.